Linux command line
From ScientificComputing
Bash is a powerful scripting language, which can directly been used in a Linux terminal. Here we give short examples
- specify a variable and print its value to the standard output
[leonhard@euler01 ~]$ VAR_A="some string variable" [leonhard@euler01 ~]$ echo $VAR_A some string variable
- Print numbers 1-5 to standard output with a for loop
[leonhard@euler01 ~]$ for i in {1..5}; do echo $i; done
1
2
3
4
5
- Print all numbers with two digits to standard output without using a for loop
[leonhard@euler01 ~]$ echo {0..9}{0..9}
00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- Print 5 random number to standard output and index them
[leonhard@euler01 test]$ for i in {1..5}; do echo "$i-th random number $RANDOM"; done
1-th random number 25702
2-th random number 21605
3-th random number 6648
4-th random number 13259
5-th random number 8814
- Do manipulations on a string (for instance exchange "home" by "work" in "/cluster/home/leonhard")
[leonhard@euler01 ~]$ STRING1="/cluster/home/leonhard"
[leonhard@euler01 ~]$ echo ${STRING1/home/work}
/cluster/work/leonhard
Linux commands
ls
- Display list of files and folders sorted by time in reversed order (newest files at the bottom), including hidden files.
[leonhard@euler01 test]$ ls -ltra total 1619 -rw-r--r-- 1 leonhard T0000 166 Jun 13 17:12 file2 -rw-r--r-- 1 leonhard T0000 26096 Jun 13 17:13 .file3 -rw-r--r-- 1 leonhard T0000 44642 Jun 13 17:14 file4 -rw-r--r-- 1 leonhard T0000 1488156 Jun 13 17:14 file1 -rw-r--r-- 1 leonhard T0000 73 Jun 13 17:15 file5 drwx------ 71 leonhard T0000 117 Jun 13 17:15 .. drwxr-xr-x 2 leonhard T0000 7 Jun 13 17:15 .
- Display list of files sorted by filesize in reversed order (largest files at the bottom), including hidden files.
[leonhard@euler01 test]$ ls -lSra total 1619 drwxr-xr-x 2 leonhard T0000 7 Jun 13 17:15 . -rw-r--r-- 1 leonhard T0000 73 Jun 13 17:15 file5 drwx------ 71 leonhard T0000 117 Jun 13 17:15 .. -rw-r--r-- 1 leonhard T0000 166 Jun 13 17:12 file2 -rw-r--r-- 1 leonhard T0000 26096 Jun 13 17:13 .file3 -rw-r--r-- 1 leonhard T0000 44642 Jun 13 17:14 file4 -rw-r--r-- 1 leonhard T0000 1488156 Jun 13 17:14 file1
cd
- Change to your home directory.
cd ~
- Go one level up in the directory hierarchy.
cd ..
- Change to a directory with path: /path/to/directory.
cd /path/to/directory
pwd
- Print working directory.
[leonhard@euler01 test]$ pwd /cluster/home/sdid/sfux/test
echo
- Print a string to the standard output.
[leonhard@euler01 test]$ echo this goes to the standard output this goes to the standard output
less, cat, more
- Display the content of a file.
less file
or
cat file
or
more file
cp
- Copy a file.
[leonhard@euler01 test]$ ls -l total 1540 -rw-r--r-- 1 leonhard T0000 1488156 Jun 13 17:14 file1 [leonhard@euler01 test]$ cp file1 file2 [leonhard@euler01 test]$ ls -l total 1540 -rw-r--r-- 1 leonhard T0000 1488156 Jun 13 17:14 file1 -rw-r--r-- 1 leonhard T0000 1488156 Jun 13 17:26 file2
- Copy a directory.
[leonhard@euler01 test]$ ls -l total 1 drwxr-xr-x 2 leonhard T0000 2 Jun 13 17:26 testdir1 [leonhard@euler01 test]$ cp -r testdir1 testdir2 [leonhard@euler01 test]$ ls -l total 2 drwxr-xr-x 2 leonhard T0000 2 Jun 13 17:26 testdir1 drwxr-xr-x 2 leonhard T0000 2 Jun 13 17:27 testdir2 [leonhard@euler01 test]$
mv
- Rename a file.
[leonhard@euler01 test]$ ls -l total 1 -rw-r--r-- 1 leonhard T0000 10 Jun 13 17:28 file1 [leonhard@euler01 test]$ mv file1 file2 [leonhard@euler01 test]$ ls -l total 1 -rw-r--r-- 1 leonhard T0000 10 Jun 13 17:28 file2
rm
- Delete a file.
[leonhard@euler01 test]$ ls -l total 1 -rw-r--r-- 1 leonhard T0000 10 Jun 13 17:28 file2 [leonhard@euler01 test]$ rm file2 [leonhard@euler01 test]$ ls -l total 0
- Delete a directory (no matter if it contains files or not).
[leonhard@euler01 test]$ ls -l total 1 drwxr-xr-x 2 sfux sdid 2 Jun 13 17:30 testdir1 [leonhard@euler01 test]$ rm -r testdir1 [leonhard@euler01 test]$ ls -l total 0
mkdir
- Create a directory.
[leonhard@euler01 test]$ ls -l total 0 [leonhard@euler01 test]$ mkdir testdir1 [leonhard@euler01 test]$ ls -l total 1 drwxr-xr-x 2 leonhard T0000 2 Jun 13 17:31 testdir1
rmdir
- Delete a directory (deletes only empty directories).
[leonhard@euler01 test]$ ls -l total 1 drwxr-xr-x 2 sfux sdid 2 Jun 13 17:31 testdir1 [leonhard@euler01 test]$ rmdir testdir1 [leonhard@euler01 test]$ ls -l total 0
man
- Display the manual of a Linux command (output is too large to display it here, but just try it out).
man ls man screen
exit
- Close your connection to Brutus.
[leonhard@euler01 ~]$ exit logout Connection to brutus.ethz.ch closed. sfux@bullvalene:~$
vi, nano
- Try out the text editors by displaying a file.
vi file
or
nano file
grep
- Search for a string within another string or a file.
[leonhard@euler01 test]$ ls -l total 2 -rw-r--r-- 1 leonhard T0000 0 Jun 13 17:44 file11 -rw-r--r-- 1 leonhard T0000 0 Jun 13 17:44 file20 -rw-r--r-- 1 leonhard T0000 0 Jun 13 17:43 testfile1 -rw-r--r-- 1 leonhard T0000 0 Jun 13 17:43 testfile2 [leonhard@euler01 test]$ ls -l | grep test -rw-r--r-- 1 leonhard T0000 0 Jun 13 17:43 testfile1 -rw-r--r-- 1 leonhard T0000 0 Jun 13 17:43 testfile2
sort
- Sort a file line by line
[leonhard@euler01 test]$ more file1 c line c b line b d line d a line a [leonhard@euler01 test]$ sort file1 a line a b line b c line c d line d
sed
- Powerful tool for string manipulation (even whole files) which has many more functions. Exchange part of a string by another one (see also bash examples)
[leonhard@euler01 test]$ echo what a beautyful day | sed s/day/night/ what a beautyful night [leonhard@euler01 test]$
awk
- Awk is really a programming language. It can process text, perform arithmetic operations, etc. It is usually used in combination with another command to process/extract information. For example, to find out how many jobs are pending/running on the cluster:
[leonhard@euler01 ~]$ bqueues
QUEUE_NAME PRIO STATUS MAX JL/U JL/P JL/H NJOBS PEND RUN SUSP
special 90 Open:Active - - - - 49 0 49 0
pub.1h 78 Open:Active - - - - 5115 3611 1504 0
pub.8h 76 Open:Active - - - - 81767 73201 8566 0
pub.36h 74 Open:Active 256 32 - - 150 73 77 0
vip.36h 74 Open:Active - 256 - - 12905 10780 2125 0
mpp.36h 74 Open:Active - 512 - - 1344 544 800 0
pub.7d 72 Open:Active 128 16 - - 590 561 29 0
vip.7d 70 Open:Active - 128 - - 1911 682 1229 0
fairshare 50 Open:Inact - - - - 0 0 0 0
purgatory 1 Open:Inact - - - - 0 0 0 0
[leonhard@euler01 ~]$ bqueues | awk 'BEGIN{p=0;r=0} NR>1{p+=$9;r+=$10} END{printf "Pending:%8i\nRunning:%8i\n",p,r}'
Pending: 89460
Running: 14371
find Search a string (substitute 'searchstring' by the string you are searching for) in all files contained in the current directory and all its subdirectories.
find . -type f -exec grep -q 'searchstring' {} \; -a -exec ls -l {} \;
du
- Go to a directory and display the total size of it and then the sizes of all subdirectories.
[leonhard@euler01 mathematica]$ du -hs 8.6M . [leonhard@euler01 mathematica]$ du -h 17K ./parallel 5.0K ./batch_mode 24K ./plot_graphics 1.3M ./ptest 7.3M ./ptest2 8.6M .
tar
- Create a tar archive including several files.
[leonhard@euler01 test]$ ls PtCO.t21 t21.C t21.O t21.Pt [leonhard@euler01 test]$ tar -cf test.tar * [leonhard@euler01 test]$ ls -ltr total 5903 -rw------- 1 leonhard T0000 675840 May 23 15:27 t21.Pt -rw------- 1 leonhard T0000 442368 May 23 15:27 t21.O -rw------- 1 leonhard T0000 442368 May 23 15:27 t21.C -rw------- 1 leonhard T0000 1204224 May 23 15:27 PtCO.t21 -rw-r--r-- 1 leonhard T0000 2775040 Jun 15 15:48 test.tar
gzip
- Compress a file or an archive (tar and gzip are often used together) using gzip.
[leonhard@euler01 test]$ ls -ltr total 2821 -rw-r--r-- 1 leonhard T0000 2775040 Jun 15 15:48 test.tar [leonhard@euler01 test]$ gzip test.tar [sfux@brutus2 test]$ ls -ltr total 1 -rw-r--r-- 1 leonhard T0000 730947 Jun 15 15:48 test.tar.gz [leonhard@euler01 test]$ gunzip test.tar.gz [leonhard@euler01 test]$ ls -ltr total 1 -rw-r--r-- 1 leonhard T0000 2775040 Jun 15 15:48 test.tar
bzip2
- Compress a file or an archive using bzip2
[leonhard@euler01 test]$ ls -ltr total 2820 -rw-r--r-- 1 leonhard T0000 2775040 Jun 15 15:48 test.tar [leonhard@euler01 test]$ bzip2 test.tar [leonhard@euler01 test]$ ls -ltr total 1 -rw-r--r-- 1 leonhard T0000 638158 Jun 15 15:48 test.tar.bz2 [leonhard@euler01 test]$ bunzip2 test.tar.bz2 [leonhard@euler01 test]$ ls -ltr total 1 -rw-r--r-- 1 leonhard T0000 2775040 Jun 15 15:48 test.tar'
